Fig. 8

Principal Coordinate Analysis of All Subject Samples Does Not Demonstrate Clustering by Subject. PCoA of the β-diversity data set using Bray-Curtis distance was performed using QIIME and R. Samples were color-coded by subject with the sample site noted by shape (see legend). Bronchial (circles) and peripheral lung samples (squares) from the same subject are connected with colored subject-specific lines. In an analysis of the 17 bronchial and peripheral lung samples only, the within-subject distance between the bronchial and peripheral lung microbiota is smaller than the between-subject distance of the bronchial and peripheral lung microbiota (permutation testing with batch correction, p = 0.0139)